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epi2me-labs / wf-clone-validation

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unknown config attribute params.projectDir #2

Closed babramso closed 2 years ago

babramso commented 2 years ago

I'm not really familiar with nextflow and unsure how to handle this.

root@MSI:/mnt/c/Users/theab/Documents# nextflow run epi2me-labs/wf-clone-validation --help N E X T F L O W ~ version 19.01.0 Launching epi2me-labs/wf-clone-validation [sharp_swartz] - revision: 4048ddebdc [master] ERROR ~ Unknown config attribute params.projectDir -- check config file: /root/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config

-- Check '.nextflow.log' file for details

Contents of the '.nextflow.log'

root@MSI:/mnt/c/Users/theab/Documents# cat .nextflow.log Nov-02 17:06:46.163 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-clone-validation --help Nov-02 17:06:46.270 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.01.0 Nov-02 17:06:46.693 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/epi2me-labs/wf-clone-validation/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-clone-validation.git Nov-02 17:06:46.701 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/epi2me-labs/wf-clone-validation/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-clone-validation.git Nov-02 17:06:46.784 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/epi2me-labs/wf-clone-validation/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-clone-validation.git Nov-02 17:06:46.784 [main] INFO nextflow.cli.CmdRun - Launching epi2me-labs/wf-clone-validation [sharp_swartz] - revision: 4048ddebdc [master] Nov-02 17:06:47.268 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /root/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config
Nov-02 17:06:47.270 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /root/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config
Nov-02 17:06:47.276 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard Nov-02 17:06:47.360 [main] DEBUG nextflow.config.ConfigBuilder - In the following config object the attribute params.projectDir is empty: help=true out_dir='output' wfversion='v0.1.4' fastq=null db_directory=null sanitize_fastq=false samples=null threads=4 host_reference='NO_HOST_REF' regions_bedfile='NO_REG_BED' approx_size=7000 assm_coverage=60 trim_length=150 canu_useGrid=false prefix=null min_barcode=null max_barcode=null primers=[:]/data/primers.tsv reference=null report_name='report' monochrome_logs=false validate_params=true show_hidden_params=false schema_ignore_params='show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wfversion'

Nov-02 17:06:47.365 [main] ERROR nextflow.cli.Launcher - Unknown config attribute params.projectDir -- check config file: /root/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config nextflow.exception.ConfigParseException: Unknown config attribute params.projectDir -- check config file: /root/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:488) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:237) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:249) at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:400) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184) at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:402) at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176) at nextflow.config.ConfigBuilder.merge0(ConfigBuilder.groovy:367) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184) at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:316) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176) at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:282) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:168) at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:633) at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:646) at nextflow.script.ScriptRunner.(ScriptRunner.groovy:121) at nextflow.cli.CmdRun.run(CmdRun.groovy:223) at nextflow.cli.Launcher.run(Launcher.groovy:445) at nextflow.cli.Launcher.main(Launcher.groovy:622)

sarahjeeeze commented 2 years ago

Hi, I think its because the version of Nextflow needs to be 20+. You can update using the cmd nextflow self-update. Also see here - https://www.nextflow.io/docs/latest/getstarted.html